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bug for bingo-elastic substructure search #2544

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jank9201 opened this issue Oct 10, 2024 · 2 comments
Open

bug for bingo-elastic substructure search #2544

jank9201 opened this issue Oct 10, 2024 · 2 comments

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@jank9201
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@Summary
it seems that bingo-elastic for substructure search is not really working

Steps to Reproduce
1.example from Substructure Search(https://lifescience.opensource.epam.com/bingo/user-manual-oracle.html)

Actual behavior
for example :
substructuresearch
searched with phenol and indexed O(Br)C1C=CC=CC=1 and phenol, only retrieved phenol

Expected behavior
Retrieve O(Br)C1C=CC=CC=1 and phenol

Environment details:
elasticsearch version 17.15.2
inidgo version 1.23.0

@AlexanderSavelyev
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could you try to aromatize input query molecule?

@jank9201
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@AlexanderSavelyev thank your reply very much, I have tested with query molecule of c1ccccc1:[o] (aromatized phenol), it did not retrieve any result, at this time, and I also tested the following example (from https://lifescience.opensource.epam.com/bingo/user-manual-oracle.html#substructure-search) :
substructuresearch2
, it still did not working, current exact and similarity search works.
the above-mentioned example of my substructure search code is:

		String smiles= "C1CC1.C1CC1";

		IndigoRecord target = Helpers.loadFromSmiles(smiles);  
      
                List<IndigoRecord> substructureMatchRecords = repository.stream()
                .filter(new SubstructureMatch<>(target))
                .collect(Collectors.toList())
                .stream()
                .filter(SubstructureMatch.substructureMatchAfterChecker(target, indigo))
                .collect(Collectors.toList());

anything is wrong?

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